Human Gene ACTN4 (ENST00000252699.7_9) from GENCODE V47lift37
  Description: actinin alpha 4, transcript variant 1 (from RefSeq NM_004924.6)
Gencode Transcript: ENST00000252699.7_9
Gencode Gene: ENSG00000130402.14_17
Transcript (Including UTRs)
   Position: hg19 chr19:39,138,289-39,222,229 Size: 83,941 Total Exon Count: 21 Strand: +
Coding Region
   Position: hg19 chr19:39,138,386-39,220,072 Size: 81,687 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:39,138,289-39,222,229)mRNA (may differ from genome)Protein (911 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ACTN4_HUMAN
DESCRIPTION: RecName: Full=Alpha-actinin-4; AltName: Full=F-actin cross-linking protein; AltName: Full=Non-muscle alpha-actinin 4;
FUNCTION: F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. This is a bundling protein. Probably involved in vesicular trafficking via its association with the CART complex. The CART complex is necessary for efficient transferrin receptor recycling but not for EGFR degradation.
SUBUNIT: Homodimer; antiparallel (By similarity). Binds TRIM3 at the N-terminus (By similarity). Identified in a complex with CASK, IQGAP1, MAGI2, NPHS1, SPTAN1 and SPTBN1 (By similarity). Identified in a mRNP granule complex, at least composed of ACTB, ACTN4, DHX9, ERG, HNRNPA1, HNRNPA2B1, HNRNPAB, HNRNPD, HNRNPL, HNRNPR, HNRNPU, HSPA1, HSPA8, IGF2BP1, ILF2, ILF3, NCBP1, NCL, PABPC1, PABPC4, PABPN1, RPLP0, RPS3, RPS3A, RPS4X, RPS8, RPS9, SYNCRIP, TROVE2, YBX1 and untranslated mRNAs. Component of the CART complex, at least composed of ACTN4, HGS/HRS, MYO5B and TRIM3. Interacts with BAIAP1 and PDLIM2.
INTERACTION: P35222:CTNNB1; NbExp=6; IntAct=EBI-351526, EBI-491549; Q07157:TJP1; NbExp=4; IntAct=EBI-351526, EBI-79553;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Colocalizes with actin stress fibers. Nuclear translocation can be induced by the PI3 kinase inhibitor wortmannin or by cytochalasin D. Exclusively localized in the nucleus in a limited number of cell lines (breast cancer cell line MCF-7, oral floor cancer IMC- 2, and bladder cancer KU-7).
TISSUE SPECIFICITY: Widely expressed.
DISEASE: Defects in ACTN4 are the cause of focal segmental glomerulosclerosis type 1 (FSGS1) [MIM:603278]. A renal pathology defined by the presence of segmental sclerosis in glomeruli and resulting in proteinuria, reduced glomerular filtration rate and edema. Renal insufficiency often progresses to end-stage renal disease, a highly morbid state requiring either dialysis therapy or kidney transplantation.
SIMILARITY: Belongs to the alpha-actinin family.
SIMILARITY: Contains 1 actin-binding domain.
SIMILARITY: Contains 2 CH (calponin-homology) domains.
SIMILARITY: Contains 2 EF-hand domains.
SIMILARITY: Contains 4 spectrin repeats.
SEQUENCE CAUTION: Sequence=AAC17470.1; Type=Frameshift; Positions=19, 26, 124, 130, 589, 594, 787, 806; Sequence=BAA24447.1; Type=Erroneous initiation;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/ACTN4";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: ACTN4
Diseases sorted by gene-association score: glomerulosclerosis, focal segmental, 1* (1650), focal segmental glomerulosclerosis (41), galloway-mowat syndrome (17), congenital nephrotic syndrome finnish type (11), hypoparathyroidism, sensorineural deafness, and renal dysplasia (9), nephrotic syndrome (8), familial nephrotic syndrome (8), frasier syndrome (8), kidney disease (4), wilms tumor susceptibility-5 (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 288.70 RPKM in Artery - Tibial
Total median expression: 3940.36 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -32.6097-0.336 Picture PostScript Text
3' UTR -816.002157-0.378 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001589 - Actinin_actin-bd_CS
IPR001715 - CH-domain
IPR011992 - EF-hand-like_dom
IPR014837 - EF-hand_Ca_insen
IPR018247 - EF_Hand_1_Ca_BS
IPR018249 - EF_HAND_2
IPR002048 - EF_hand_Ca-bd
IPR018159 - Spectrin/alpha-actinin
IPR002017 - Spectrin_repeat

Pfam Domains:
PF00307 - Calponin homology (CH) domain
PF00435 - Spectrin repeat
PF08726 - Ca2+ insensitive EF hand
PF11971 - CAMSAP CH domain
PF13833 - EF-hand domain pair

SCOP Domains:
47473 - EF-hand
47576 - Calponin-homology domain, CH-domain
46966 - Spectrin repeat
143847 - XisI-like
58014 - Coiled-coil domain of nucleotide exchange factor GrpE

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WLX - NMR MuPIT 1YDI - X-ray MuPIT 2R0O - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O43707
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0001882 nucleoside binding
GO:0003723 RNA binding
GO:0003779 actin binding
GO:0005178 integrin binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity
GO:0031490 chromatin DNA binding
GO:0035257 nuclear hormone receptor binding
GO:0042803 protein homodimerization activity
GO:0042974 retinoic acid receptor binding
GO:0044325 ion channel binding
GO:0044877 macromolecular complex binding
GO:0046872 metal ion binding
GO:0047485 protein N-terminus binding
GO:0051015 actin filament binding

Biological Process:
GO:0001666 response to hypoxia
GO:0002576 platelet degranulation
GO:0015031 protein transport
GO:0030050 vesicle transport along actin filament
GO:0030335 positive regulation of cell migration
GO:0032417 positive regulation of sodium:proton antiporter activity
GO:0035357 peroxisome proliferator activated receptor signaling pathway
GO:0042981 regulation of apoptotic process
GO:0048384 retinoic acid receptor signaling pathway
GO:0048549 positive regulation of pinocytosis
GO:0051017 actin filament bundle assembly
GO:0051271 negative regulation of cellular component movement
GO:0051272 positive regulation of cellular component movement
GO:0070830 bicellular tight junction assembly
GO:1900025 negative regulation of substrate adhesion-dependent cell spreading
GO:1901224 positive regulation of NIK/NF-kappaB signaling
GO:1902396 protein localization to bicellular tight junction
GO:1903506 regulation of nucleic acid-templated transcription

Cellular Component:
GO:0001725 stress fiber
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005903 brush border
GO:0005911 cell-cell junction
GO:0005925 focal adhesion
GO:0016604 nuclear body
GO:0030018 Z disc
GO:0030054 cell junction
GO:0030863 cortical cytoskeleton
GO:0031093 platelet alpha granule lumen
GO:0031143 pseudopodium
GO:0032991 macromolecular complex
GO:0043005 neuron projection
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome
GO:1990904 ribonucleoprotein complex
GO:0015629 actin cytoskeleton


-  Descriptions from all associated GenBank mRNAs
  AK309363 - Homo sapiens cDNA, FLJ99404.
U48734 - Human non-muscle alpha-actinin mRNA, complete cds.
AK309361 - Homo sapiens cDNA, FLJ99402.
AK309364 - Homo sapiens cDNA, FLJ99405.
AK299955 - Homo sapiens cDNA FLJ61380 complete cds, highly similar to Alpha-actinin-4.
AK304554 - Homo sapiens cDNA FLJ58087 complete cds, highly similar to Alpha-actinin-4.
BX647098 - Homo sapiens mRNA; cDNA DKFZp686K23158 (from clone DKFZp686K23158).
BC005033 - Homo sapiens actinin, alpha 4, mRNA (cDNA clone MGC:12692 IMAGE:3842046), complete cds.
GU987085 - Homo sapiens alpha actinin 4 short isoform (ACTN4) mRNA, complete cds.
CU678876 - Synthetic construct Homo sapiens gateway clone IMAGE:100017838 5' read ACTN4 mRNA.
AB590161 - Synthetic construct DNA, clone: pFN21AE1354, Homo sapiens ACTN4 gene for actinin, alpha 4, without stop codon, in Flexi system.
KU177881 - Homo sapiens actinin alpha 4 isoform 1 (ACTN4) mRNA, partial cds.
KU177882 - Homo sapiens actinin alpha 4 isoform 2 (ACTN4) mRNA, partial cds, alternatively spliced.
KU177883 - Homo sapiens actinin alpha 4 isoform 3 (ACTN4) mRNA, partial cds, alternatively spliced.
KU177884 - Homo sapiens actinin alpha 4 isoform 4 (ACTN4) mRNA, complete cds, alternatively spliced.
DQ893439 - Synthetic construct clone IMAGE:100006069; FLH199530.01X; RZPDo839H0382D actinin, alpha 4 (ACTN4) gene, encodes complete protein.
DQ896777 - Synthetic construct Homo sapiens clone IMAGE:100011237; FLH199437.01L; RZPDo839H0381D actinin, alpha 4 (ACTN4) gene, encodes complete protein.
KJ890622 - Synthetic construct Homo sapiens clone ccsbBroadEn_00016 ACTN4 gene, encodes complete protein.
KR710084 - Synthetic construct Homo sapiens clone CCSBHm_00009354 ACTN4 (ACTN4) mRNA, encodes complete protein.
KR710085 - Synthetic construct Homo sapiens clone CCSBHm_00009355 ACTN4 (ACTN4) mRNA, encodes complete protein.
KR710086 - Synthetic construct Homo sapiens clone CCSBHm_00009356 ACTN4 (ACTN4) mRNA, encodes complete protein.
KR710087 - Synthetic construct Homo sapiens clone CCSBHm_00009357 ACTN4 (ACTN4) mRNA, encodes complete protein.
DQ431186 - Homo sapiens actinin alpha4 isoform (ACTN4) mRNA, complete cds, alternatively spliced.
D89980 - Homo sapiens mRNA for alpha actinin 4, complete cds.
JD484932 - Sequence 465956 from Patent EP1572962.
JD336693 - Sequence 317717 from Patent EP1572962.
BC015620 - Homo sapiens actinin, alpha 4, mRNA (cDNA clone IMAGE:4843317), partial cds.
Z36797 - H.sapiens (xs146) mRNA, 400bp.
DL492155 - Novel nucleic acids.
LF207581 - JP 2014500723-A/15084: Polycomb-Associated Non-Coding RNAs.
LF367263 - JP 2014500723-A/174766: Polycomb-Associated Non-Coding RNAs.
JD122878 - Sequence 103902 from Patent EP1572962.
JD419269 - Sequence 400293 from Patent EP1572962.
DQ577444 - Homo sapiens piRNA piR-45556, complete sequence.
MA602840 - JP 2018138019-A/174766: Polycomb-Associated Non-Coding RNAs.
MA443158 - JP 2018138019-A/15084: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O43707 (Reactome details) participates in the following event(s):

R-HSA-481007 Exocytosis of platelet alpha granule contents
R-HSA-451403 Interaction of nephrin with adherens junction-associated proteins
R-HSA-114608 Platelet degranulation
R-HSA-373753 Nephrin family interactions
R-HSA-76005 Response to elevated platelet cytosolic Ca2+
R-HSA-1500931 Cell-Cell communication
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: A4K467, ACTN4 , ACTN4_HUMAN, D6PXK4, ENST00000252699.1, ENST00000252699.2, ENST00000252699.3, ENST00000252699.4, ENST00000252699.5, ENST00000252699.6, NM_004924, O43707, O76048, uc317fig.1, uc317fig.2
UCSC ID: ENST00000252699.7_9
RefSeq Accession: NM_004924.6
Protein: O43707 (aka ACTN4_HUMAN or AAC4_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.